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Factor out small community detection #51

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Factor out small community detection #51

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Commits on Feb 20, 2024

  1. Merge pull request #1 from ahill187/fix-simplicial-set-embedding-bug 

    Fix simplicial set embedding bug
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Commits on Aug 11, 2024

  1. create a custom logger

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  2. replace all print statements with logging statements

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  3. remove commented print statements

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  4. Merge remote-tracking branch 'upstream/master'

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  5. Merge pull request #8 from ahill187/logging 

    Add logging
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  6. fix code line layout

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  7. remove unnecessary ==True and ==False

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  8. remove unnecessary dummy variables

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  9. remove unused variables

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  10. clean up comments

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  11. make strings consistent

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  12. make strings consistent

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  13. remove trailing whitespace

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  14. update gitignore

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  15. Merge branch 'code-cleanup' of https://github.com/ahill187/PARC into … 

    …code-cleanup
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  16. rearrange run_toobig_PARC signature

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  17. Merge pull request #9 from ahill187/code-cleanup 

    Code cleanup
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  18. move func_mode to utils

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  19. add test for get_mode

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  20. modify get_mode docstring

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  21. Merge pull request #10 from ahill187/func-mode 

    `func_mode` -> `get_mode`
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Commits on Aug 12, 2024

  1. rename X_data, X_input, data -> x_data

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  2. rename true_label, true_labels -> y_data_true

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  3. rename PARC_labels, labels -> y_data_pred

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  4. rename PARC_labels_array -> y_data_pred_array

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  5. rename num_threads -> n_threads

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  6. rename N, n_cells, n_elements -> n_samples

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  7. rename small_pop -> small_community_size

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  8. rename time_smallpop -> small_community_timeout

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  9. rename time_smallpop_start -> time_start

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  10. rename small_pop_exist -> small_community_exists

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  11. rename too_big_factor -> large_community_factor

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  12. rename distance -> distance_metric

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  13. rename dist_std_local -> l2_std_factor

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  14. rename jac_std_global, jac_std_toobig -> jac_std_factor

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  15. rename G -> graph

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  16. rename G_sim -> graph_pruned

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  17. rename sim_list -> similarities

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  18. rename sim_list_new -> similarities_new

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  19. rename sim_list_array -> similarities_array

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  20. rename edgelist -> edges

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  21. rename edgelist_copy -> edges_copy

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  22. rename new_edgelist -> new_edges

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  23. remove edge_list_copy_array

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  24. rename strong_locs -> indices_similar

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  25. rename PARC_labels_leiden -> node_communities

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  26. rename PARC_labels_leiden_big -> node_communities_big

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  27. rename set_PARC_labels_leiden -> set_node_communities

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  28. rename cluster_ii -> community_id

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  29. rename pop_i, pop_ii -> community_size

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  30. rename cluster_i_loc, cluster_ii_loc -> community_indices

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  31. rename cluster_big_loc -> large_community_indices

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  32. rename cluster_big -> large_community_id

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  33. rename big_pop -> large_community_size

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  34. rename n_cancer -> n_target

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  35. rename cluster_i -> community_id

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  36. rename pbmc_labels -> negative_labels

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  37. rename thp1_labels -> positive_labels

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  38. rename onevsall, onevsall_val -> target

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  39. rename sources -> input_nodes

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  40. rename targets -> output_nodes

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  41. remove X_data_big

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  42. Merge pull request #11 from ahill187/variable-renaming 

    Rename variables
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  43. add docstrings to constructor

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  44. change default keep_all_local_dist to None

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  45. create setter for keep_all_local_dist

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  46. fix bug from last commit

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  47. add partition_type setter

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  48. add setter for y_data_true

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  49. add typehints for constructor

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  50. clean up the Attributes section

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  51. Merge pull request #12 from ahill187/constructor 

    Add docstrings and properties to the constructor
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  52. factor out compute_performance_metrics

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  53. rename time_start_total -> time_start

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  54. remove run_subPARC

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  55. Merge pull request #13 from ahill187/compute-performance-metrics 

    Factor out `compute_performance_metrics`
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  56. rename run_PARC -> run_parc

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  57. simplify find_partition logic

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  58. update logs

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  59. factor out get_leiden_partition

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  60. add tests for get_leiden_partition

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  61. Merge pull request #14 from ahill187/get-leiden-partition 

    Factor out `get_leiden_partition`
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  62. rename knngraph_full to create_knn_graph

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  63. clean up create_knn_graph

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  64. rename k_umap -> knn

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  65. set knn as argument

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Commits on Aug 13, 2024

  1. add tests for create_knn_graph

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  2. rename graph -> csr_array

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  3. Merge pull request #15 from ahill187/create-knn-graph 

    Refactor `knngraph_full` -> `create_knn_graph`
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  4. Rename make_csrmatrix_noselfloop -> prune_local

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  5. rename keep_all_local_dist -> do_prune_local

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  6. remove unused discard_count

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  7. remove unnecessary comments

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  8. rename distlist -> distances

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  9. add max_distance

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  10. rename row -> neighbors

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  11. rename updated_nn_ind -> updated_neighbors

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  12. rename updated_nn_weights -> updated_distances

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  13. rename ik -> index

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  14. rename rowi -> community_id

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  15. rename csr_graph -> csr_array

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  16. rename dist -> distance

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  17. clean up the prune_local function

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  18. add l2_std_factor as argument to prune_local

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  19. add tests for prune_local

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  20. Merge pull request #16 from ahill187/prune-local 

    Refactor `prune_local`
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  21. add jac_threshold_type

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  22. Merge pull request #17 from ahill187/jac-threshold-type 

    New argument `jac_threshold_type`
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  23. create new function prune_global

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  24. factor out prune_global from run_parc

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  25. factor out prune_global from run_toobig_subPARC

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  26. modify the log messages

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  27. add tests for prune_global

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  28. remove similarities_new

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  29. remove new_edges

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  30. remove similarities_array

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  31. docstring cleanup

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  32. Merge pull request #18 from ahill187/prune-global 

    Factor out `prune_global`
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  33. rename hnsw -> knn_struct

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  34. change x_data to parameter and removed big_cluster

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  35. rename num_dims -> n_features

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  36. move n_featuers, n_samples, add_items

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  37. add distance_metric parameter

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  38. move hnswlib.Index call

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  39. move init_index

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  40. change n_threads to parameter

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  41. change M to parameter

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  42. convert ef_construction to parameter

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  43. rename p -> knn_struct

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  44. add knn as parameter

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  45. add docstrings

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  46. add ef_query as parameter and remove too_big

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  47. remove unnecessary comment

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  48. update the docstrings

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  49. add tests for make_knn_struct

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  50. Merge pull request #19 from ahill187/refactor-knn-struct-2 

    Refactor `make_knn_struct`
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  51. fix small_community_size bug

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  52. Merge pull request #20 from ahill187/small-community-size 

    Fix `small_community_size` bug
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Commits on Aug 14, 2024

  1. add tests for run_parc

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  2. add pytest.ini

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  3. fix & bug

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  4. add large_community_id

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  5. update log messages

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  6. rearrange constructor to match order of attributes

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Commits on Aug 30, 2024

  1. add tests_workflow

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  2. fix bugs in tests

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  3. cancel tests if one fails

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  4. change default logging level to 25

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  5. Merge pull request #21 from ahill187/tests 

    Tests
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  6. add x_data setter

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  7. modify the y_data_true setter

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  8. add y_data_pred setter

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  9. allow x_data to be passed in as pd.DataFrame

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  10. fix y_data_true setter

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  11. Merge pull request #22 from ahill187/input-data-types 

    Input data types
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Commits on Aug 31, 2024

  1. clean up setup.py

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  2. add requirements.txt

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  3. Merge pull request #23 from ahill187/requirements-setup 

    `requirements.txt` and `setup.py`
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Commits on Nov 9, 2024

  1. rename run_parc -> fit_predict

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  2. refactor pop_list -> community_counts

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Commits on Nov 11, 2024

  1. convert logging message to info

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  2. add docstrings to fit_predict

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  3. move time_start to top

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  4. Merge pull request #25 from ahill187/fit 

    Fit
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  5. add save function to PARC

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  6. add tests for save model

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  7. add load function

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  8. test load function

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Commits on Nov 13, 2024

  1. Merge pull request #26 from ahill187/save-model 

    Add save/load model options
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  2. rename create_knn_struct -> create_hnsw_index

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  3. rename knn_struct -> hnsw_index

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  4. update logging

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  5. move ef_query settings to create_hnsw_index

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  6. update ef_query in run_toobig_subPARC

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  7. Create pull_request_template.md

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  8. Delete .github/workflows/pull_request_template.md

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  9. Create pull_request_template.md

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  10. Merge pull request #27 from ahill187/hnswlib 

    Modify `create_hnsw_index`
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Commits on Nov 14, 2024

  1. remove unnecessary reshaping

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  2. remove unnecessary np.asarray call

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  3. clean up node communities call

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  4. factor out get_next_large_community

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  5. remove unnecessary node communities transformation

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  6. factor out large community detection

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  7. add test for large community expansion

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  8. Merge pull request #28 from ahill187/large-communities 

    Factor out large community expansion
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  9. move small community detection into small_community_merging

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  10. factor out small_community_merging from run_toobig_subPARC

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  11. rename cluster -> community_id

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  12. rename population -> community_size

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  13. add community_indices

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  14. rename small_cluster to small_community_indices

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  15. rename single_cell to sample_id

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  16. refactor small_communities

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  17. rename old_neighbors -> neighbors

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  18. rename group_of_old_neighbors -> node_communities_neighbors

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  19. refactor available neighbors list

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  20. rename best_group to community_id

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  21. remove unnecessary list, flatten call

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  22. factor out reassign_small_communities

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  23. fix indentation error

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  24. factor out get_small_communities

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  25. rename time_start_sc to time_start

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  26. add docstrings / comments

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  27. convert small_community_timeout to parameter

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  28. fix double negative

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  29. fix bug in node_communities type

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  30. add tests for small_community_merging

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  31. add test for get_small_communities

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  32. add test for reassign_small_communities

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